Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015109.1 Kokia drynarioides strain JFW-HI SEQ_130153, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 53780
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Warning! 57 characters in sequence are not A, C, G, or T
Found at i:6027 original size:163 final size:163
Alignment explanation
Indices: 5757--6079 Score: 646
Period size: 163 Copynumber: 2.0 Consensus size: 163
5747 ATCTATCATT
5757 ATAAATTTGAATTAAACAATTTATTCACTTAATATCTTGATCCGTAGAAATTCCCAAATTATATT
1 ATAAATTTGAATTAAACAATTTATTCACTTAATATCTTGATCCGTAGAAATTCCCAAATTATATT
5822 AATGCCTCTATTCAAGCATAAAAACAATAGACTTTAAATTGATTAATTGAAATTTATTTCTAATT
66 AATGCCTCTATTCAAGCATAAAAACAATAGACTTTAAATTGATTAATTGAAATTTATTTCTAATT
5887 AAAACCCCTATTGTCGCATTAACTCGATCTTGA
131 AAAACCCCTATTGTCGCATTAACTCGATCTTGA
5920 ATAAATTTGAATTAAACAATTTATTCACTTAATATCTTGATCCGTAGAAATTCCCAAATTATATT
1 ATAAATTTGAATTAAACAATTTATTCACTTAATATCTTGATCCGTAGAAATTCCCAAATTATATT
5985 AATGCCTCTATTCAAGCATAAAAACAATAGACTTTAAATTGATTAATTGAAATTTATTTCTAATT
66 AATGCCTCTATTCAAGCATAAAAACAATAGACTTTAAATTGATTAATTGAAATTTATTTCTAATT
6050 AAAACCCCTATTGTCGCATTAACTCGATCT
131 AAAACCCCTATTGTCGCATTAACTCGATCT
6080 ATAGATTCTC
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
163 160 1.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (163 bp):
ATAAATTTGAATTAAACAATTTATTCACTTAATATCTTGATCCGTAGAAATTCCCAAATTATATT
AATGCCTCTATTCAAGCATAAAAACAATAGACTTTAAATTGATTAATTGAAATTTATTTCTAATT
AAAACCCCTATTGTCGCATTAACTCGATCTTGA
Found at i:9239 original size:28 final size:29
Alignment explanation
Indices: 9191--9247 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
9181 CGACGGATAA
* * *
9191 ATAATAATTAAATAAATAATTTTAAAATT
1 ATAAAAATTAAATAAAAAATTTAAAAATT
9220 ATAAAAATT-AATAAAAAATTTAAAAATT
1 ATAAAAATTAAATAAAAAATTTAAAAATT
9248 GGTTCAGTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
ATAAAAATTAAATAAAAAATTTAAAAATT
Found at i:13225 original size:78 final size:78
Alignment explanation
Indices: 13112--13489 Score: 434
Period size: 78 Copynumber: 4.8 Consensus size: 78
13102 AGTTAACTGG
* * * * * *
13112 ATCAATTACTTAAAAGG-CTAATGATTACAACATATTTATTCTAATCTTGACACTCCCCCATAAA
1 ATCAATTACTT--AAGGTC-AAAGATTACAACATATTTCTTTTAATCTCGACACTCCCCCACAAG
*
13176 TTAACTAGATCCTAAT
63 TTAACTGGATCCTAAT
* * * *
13192 ATCAATTATTTAAGGTCAAAGGTTACAATATATTTCTTTTAATCTCGACATTCCCCCACAAGTTA
1 ATCAATTACTTAAGGTCAAAGATTACAACATATTTCTTTTAATCTCGACACTCCCCCACAAGTTA
* *
13257 ATTGGATCTTAAT
66 ACTGGATCCTAAT
* * * *
13270 ATCAATTACTTAAAGTCAAATATTATAACATATTTCTTTTAATCTCGACACTCCCACACAAGTTA
1 ATCAATTACTTAAGGTCAAAGATTACAACATATTTCTTTTAATCTCGACACTCCCCCACAAGTTA
* **
13335 ACTGAATTTTAAT
66 ACTGGATCCTAAT
** * * *
13348 ATCAATTACTTAAGGTTGAAGATTACAACATATTTCATTTAATCTCGACATTCCCTCACAAGTTA
1 ATCAATTACTTAAGGTCAAAGATTACAACATATTTCTTTTAATCTCGACACTCCCCCACAAGTTA
* *
13413 ATTGGATTCTAAT
66 ACTGGATCCTAAT
* * * * *
13426 ATCAATTACTTAAGGTAAAAGATTATAACATATATCTTTTAATCTTGACACTCCTCCACAAGTT
1 ATCAATTACTTAAGGTCAAAGATTACAACATATTTCTTTTAATCTCGACACTCCCCCACAAGTT
13490 GGTGTGTAGA
Statistics
Matches: 253, Mismatches: 44, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
78 242 0.96
79 1 0.00
80 10 0.04
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.37
Consensus pattern (78 bp):
ATCAATTACTTAAGGTCAAAGATTACAACATATTTCTTTTAATCTCGACACTCCCCCACAAGTTA
ACTGGATCCTAAT
Found at i:13353 original size:156 final size:155
Alignment explanation
Indices: 13112--13489 Score: 490
Period size: 156 Copynumber: 2.4 Consensus size: 155
13102 AGTTAACTGG
* * * * * * *
13112 ATCAATTACTTAAAAGGCTAATGATTACAACATATTTATTCTAATCTTGACACTCCCCCATAAAT
1 ATCAATTACTT-AAAGTCAAAT-ATTATAACATATTTCTTTTAATCTTGACACT-CCCCACAAGT
* * * *
13177 TAACTAGATCCTAATATCAATTATTTAAGGTCAAAGGTTACAATATATTTCTTTTAATCTCGACA
63 TAACTAGATCCTAATATCAATTACTTAAGGTCAAAGATTACAACATATTTCATTTAATCTCGACA
13242 TTCCCCCACAAGTTAATTGGA-TCTTAAT
128 TTCCCCCACAAGTTAATTGGATTC-TAAT
*
13270 ATCAATTACTTAAAGTCAAATATTATAACATATTTCTTTTAATCTCGACACTCCCACACAAGTTA
1 ATCAATTACTTAAAGTCAAATATTATAACATATTTCTTTTAATCTTGACACTCCC-CACAAGTTA
** **
13335 ACT-GAATTTTAATATCAATTACTTAAGGTTGAAGATTACAACATATTTCATTTAATCTCGACAT
65 ACTAG-ATCCTAATATCAATTACTTAAGGTCAAAGATTACAACATATTTCATTTAATCTCGACAT
*
13399 TCCCTCACAAGTTAATTGGATTCTAAT
129 TCCCCCACAAGTTAATTGGATTCTAAT
* * * *
13426 ATCAATTACTTAAGGTAAAAGATTATAACATATATCTTTTAATCTTGACACTCCTCCACAAGTT
1 ATCAATTACTTAAAGTCAAATATTATAACATATTTCTTTTAATCTTGACACTCC-CCACAAGTT
13490 GGTGTGTAGA
Statistics
Matches: 194, Mismatches: 22, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
155 4 0.02
156 168 0.87
157 11 0.06
158 11 0.06
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.37
Consensus pattern (155 bp):
ATCAATTACTTAAAGTCAAATATTATAACATATTTCTTTTAATCTTGACACTCCCCACAAGTTAA
CTAGATCCTAATATCAATTACTTAAGGTCAAAGATTACAACATATTTCATTTAATCTCGACATTC
CCCCACAAGTTAATTGGATTCTAAT
Found at i:15743 original size:61 final size:60
Alignment explanation
Indices: 15678--15796 Score: 130
Period size: 60 Copynumber: 2.0 Consensus size: 60
15668 TATTTTTATC
** * * * *
15678 GAAAAATAAATTTTTAATTTTTTTTAAATTTTTAAGAAGTAAAATTATATTGATAAAATGT
1 GAAAAATAAAGGTTTAA-ATTTATTAAATTTTTAAGAAGTAAAACTAAATTGATAAAATGT
* ** * *
15739 GAAAAGTTGAGGTTTAAATTTATTAAATTTTTTAGAATTAAAACTAAATTGATAAAAT
1 GAAAAATAAAGGTTTAAATTTATTAAATTTTTAAGAAGTAAAACTAAATTGATAAAAT
15797 TTATAAACAT
Statistics
Matches: 47, Mismatches: 11, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
60 35 0.74
61 12 0.26
ACGTcount: A:0.46, C:0.01, G:0.10, T:0.43
Consensus pattern (60 bp):
GAAAAATAAAGGTTTAAATTTATTAAATTTTTAAGAAGTAAAACTAAATTGATAAAATGT
Found at i:30376 original size:59 final size:58
Alignment explanation
Indices: 30269--30380 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 58
30259 ATATGAAAAT
* *
30269 ATTTTATTTGAGCATATTCAAAAATATTTGACCATTATTTAATCATTTTAAAATGTTTG
1 ATTTTATTTGAGCACATTCAAAAATATTTAACCATTATTT-ATCATTTTAAAATGTTTG
30328 ATTTTATTTGAGCACATTCTAAAAA-ATTTAACTC-TTATTT-TGCAATTTTAAAA
1 ATTTTATTTGAGCACATTC-AAAAATATTTAAC-CATTATTTAT-C-ATTTTAAAA
30381 AATTTTAATC
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
57 1 0.02
58 1 0.02
59 39 0.83
60 6 0.13
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (58 bp):
ATTTTATTTGAGCACATTCAAAAATATTTAACCATTATTTATCATTTTAAAATGTTTG
Found at i:34050 original size:45 final size:45
Alignment explanation
Indices: 33995--34081 Score: 122
Period size: 45 Copynumber: 1.9 Consensus size: 45
33985 AAACTGGAGG
*
33995 TGGTGAGGGTGGAGACTTGTACTTGTAAGGG-TGCTTGGGTGGTGA
1 TGGTGAGGGTGGAGACTTGTACTCGT-AGGGATGCTTGGGTGGTGA
* * *
34040 TGGTGGGGGTGGGGACTTGTACTCGTAGGGATTCTTGGGTGG
1 TGGTGAGGGTGGAGACTTGTACTCGTAGGGATGCTTGGGTGG
34082 CGNNNNNNNN
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
44 4 0.11
45 33 0.89
ACGTcount: A:0.13, C:0.08, G:0.48, T:0.31
Consensus pattern (45 bp):
TGGTGAGGGTGGAGACTTGTACTCGTAGGGATGCTTGGGTGGTGA
Found at i:34204 original size:45 final size:45
Alignment explanation
Indices: 34155--34388 Score: 257
Period size: 45 Copynumber: 5.3 Consensus size: 45
34145 ACTTGTAGAC
*
34155 TGGTGCTGGTGGGGGTGGAGACTTGTACTTGTAAGGGTGCTTGGG
1 TGGTGATGGTGGGGGTGGAGACTTGTACTTGTAAGGGTGCTTGGG
* * * * *
34200 TGGTGATGGTGGGGGTGGGGACTTGTACTCGTAGGGGTGTTTGAG
1 TGGTGATGGTGGGGGTGGAGACTTGTACTTGTAAGGGTGCTTGGG
*
34245 TGGTGATGGTGGTGGTGGTGGGGACTTGTACTTGT-AGGGATGCTTGGG
1 TGGTGATGGT-G-GG-GGTGGAGACTTGTACTTGTAAGGG-TGCTTGGG
** * * *
34293 TGGTGACAGTGGTGGAGGAGACTTGTACTTGTAA-GATGCTTGGG
1 TGGTGATGGTGGGGGTGGAGACTTGTACTTGTAAGGGTGCTTGGG
* *
34337 TGGTGATGGT---GGAGG-GACTTGTACTTGTAA-GATGCTTGGG
1 TGGTGATGGTGGGGGTGGAGACTTGTACTTGTAAGGGTGCTTGGG
34377 TGGTGATGGTGG
1 TGGTGATGGTGG
34389 AGGAGGTGGT
Statistics
Matches: 164, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
40 35 0.21
41 5 0.03
44 16 0.10
45 67 0.41
46 3 0.02
47 6 0.04
48 32 0.20
ACGTcount: A:0.14, C:0.07, G:0.47, T:0.32
Consensus pattern (45 bp):
TGGTGATGGTGGGGGTGGAGACTTGTACTTGTAAGGGTGCTTGGG
Found at i:34367 original size:40 final size:40
Alignment explanation
Indices: 34252--34391 Score: 203
Period size: 40 Copynumber: 3.4 Consensus size: 40
34242 GAGTGGTGAT
* *
34252 GGTGGTGGTGGT-G-GGGACTTGTACTTGTAGGGATGCTTG
1 GGTGGTGATGGTGGAGGGACTTGTACTTGTA-AGATGCTTG
34291 GGTGGTGACAGTGGTGGAGGAGACTTGTACTTGTAAGATGCTTG
1 GGTGGTG--A-TGGTGGAGG-GACTTGTACTTGTAAGATGCTTG
34335 GGTGGTGATGGTGGAGGGACTTGTACTTGTAAGATGCTTG
1 GGTGGTGATGGTGGAGGGACTTGTACTTGTAAGATGCTTG
34375 GGTGGTGATGGTGGAGG
1 GGTGGTGATGGTGGAGG
34392 AGGTGGTGGA
Statistics
Matches: 93, Mismatches: 2, Indels: 11
0.88 0.02 0.10
Matches are distributed among these distances:
39 7 0.08
40 40 0.43
41 9 0.10
42 5 0.05
43 1 0.01
44 17 0.18
45 14 0.15
ACGTcount: A:0.16, C:0.07, G:0.46, T:0.31
Consensus pattern (40 bp):
GGTGGTGATGGTGGAGGGACTTGTACTTGTAAGATGCTTG
Found at i:35473 original size:29 final size:30
Alignment explanation
Indices: 35431--35744 Score: 288
Period size: 30 Copynumber: 10.6 Consensus size: 30
35421 TTTGGGGTTG
*
35431 AAAATGGAATTTTTGGAAGTTTCGAGGCCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTCA
** *
35461 AAAATGG-ATTTTTCATAAGTTTACGGGGT-A
1 AAAATGGAATTTTT-GGAAGTTT-CGAGGTCA
* *
35491 AAAATGGAATTTTTGGAA-TTTCGGGGGTAA
1 AAAATGGAATTTTTGGAAGTTTC-GAGGTCA
* * * *
35521 AAAATAGAAATTTTGGAAGTTTAGGGGT-A
1 AAAATGGAATTTTTGGAAGTTTCGAGGTCA
*
35550 AAAATGGAATTTTTGGAAGTTTCGAGGCCAA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTC-A
* * *
35581 AAAATGGAATTTTTAGAAG-TTCGGGGGTAA
1 AAAATGGAATTTTTGGAAGTTTC-GAGGTCA
* * * *
35611 AAAATAGAAATTTTGGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTCA
* *
35641 AAAATGGAATTTTTTGAAG-TTCAAGGGT-A
1 AAAATGGAATTTTTGGAAGTTTCGA-GGTCA
* *
35670 AAAATAGAATTTTTGGAAGTTTTGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTCA
*
35700 AAAATGGTA-TTTTGGAAGTTT-GATGGT-A
1 AAAATGGAATTTTTGGAAGTTTCGA-GGTCA
35728 AAAATGGAATTTTTGGA
1 AAAATGGAATTTTTGGA
35745 CGGTTTAGGA
Statistics
Matches: 233, Mismatches: 36, Indels: 31
0.78 0.12 0.10
Matches are distributed among these distances:
28 12 0.05
29 83 0.36
30 101 0.43
31 37 0.16
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.33
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTCGAGGTCA
Found at i:35502 original size:60 final size:58
Alignment explanation
Indices: 35431--35744 Score: 328
Period size: 60 Copynumber: 5.3 Consensus size: 58
35421 TTTGGGGTTG
* *
35431 AAAATGGAATTTTTGGAAGTTTCGAGGCCAAAAATGGATTTTTCATAAGTTTACGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGATTTTT-AGAAGTTTA-GGGGTA
* * * * *
35491 AAAATGGAATTTTTGGAA-TTTCGGGGGTAAAAAATAGAAATTTTGGAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTC-GAGGTCAAAAAT-GGATTTTTAGAAGTTTAGGGGTA
* **
35550 AAAATGGAATTTTTGGAAGTTTCGAGGCCAAAAAATGGAATTTTTAGAAGTTCGGGGGTAA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTC-AAAAATGG-ATTTTTAGAAGTTTAGGGGT-A
* * * * * * *
35611 AAAATAGAAATTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTTGAAGTTCAAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGG-ATTTTTAGAAGTTTAGGGGTA
* * * *
35670 AAAATAGAATTTTTGGAAGTTTTGAGGTCAAAAATGG-TATTTTGGAAGTTT-GATGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAT-TTTTAGAAGTTTAG-GGGTA
35728 AAAATGGAATTTTTGGA
1 AAAATGGAATTTTTGGA
35745 CGGTTTAGGA
Statistics
Matches: 216, Mismatches: 30, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
57 1 0.00
58 30 0.14
59 68 0.31
60 86 0.40
61 31 0.14
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.33
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGATTTTTAGAAGTTTAGGGGTA
Found at i:37626 original size:12 final size:11
Alignment explanation
Indices: 37620--37709 Score: 87
Period size: 11 Copynumber: 7.9 Consensus size: 11
37610 TTTAATTTTG
37620 AAATTAAATTT
1 AAATTAAATTT
37631 AAATTTAAATTT
1 AAA-TTAAATTT
37643 AAATTTAAA-TT
1 AAA-TTAAATTT
37654 AAATTTAAATTT
1 AAA-TTAAATTT
37666 AAGATT-AATTT
1 AA-ATTAAATTT
*
37677 AAATTTAAA-AT
1 AAA-TTAAATTT
37688 AAATCTAAATTT
1 AAAT-TAAATTT
*
37700 AAAATAAATT
1 AAATTAAATT
37710 AAAAAAAGGG
Statistics
Matches: 69, Mismatches: 3, Indels: 14
0.80 0.03 0.16
Matches are distributed among these distances:
10 2 0.03
11 37 0.54
12 29 0.42
13 1 0.01
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (11 bp):
AAATTAAATTT
Found at i:37632 original size:6 final size:6
Alignment explanation
Indices: 37610--37702 Score: 106
Period size: 6 Copynumber: 16.0 Consensus size: 6
37600 TAATTGAATT
*
37610 TTTAAT TTTGAAA -TTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
37657 TTTAAA TTTAAGA -TT-AA TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
37703 ATAAATTAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
4 1 0.01
5 15 0.20
6 57 0.75
7 3 0.04
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:37655 original size:17 final size:17
Alignment explanation
Indices: 37623--37709 Score: 122
Period size: 17 Copynumber: 5.1 Consensus size: 17
37613 AATTTTGAAA
37623 TTAAATTTAAATTTAAAT
1 TTAAATTTAAA-TTAAAT
37641 TTAAATTTAAATTAAAT
1 TTAAATTTAAATTAAAT
37658 TTAAATTTAAGATT-AAT
1 TTAAATTTAA-ATTAAAT
*
37675 TTAAATTTAAAATAAAT
1 TTAAATTTAAATTAAAT
* *
37692 CTAAATTTAAAATAAAT
1 TTAAATTTAAATTAAAT
37709 T
1 T
37710 AAAAAAAGGG
Statistics
Matches: 64, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
16 2 0.03
17 48 0.75
18 14 0.22
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (17 bp):
TTAAATTTAAATTAAAT
Found at i:37655 original size:23 final size:23
Alignment explanation
Indices: 37610--37702 Score: 111
Period size: 23 Copynumber: 4.0 Consensus size: 23
37600 TAATTGAATT
*
37610 TTTAATTTTGAAATTAAATTTAAA
1 TTTAAATTT-AAATTAAATTTAAA
37634 TTTAAATTTAAATTTAAA-TTAAA
1 TTTAAATTTAAA-TTAAATTTAAA
37657 TTTAAATTTAAGATT-AATTTAAA
1 TTTAAATTTAA-ATTAAATTTAAA
*
37680 TTTAAA-ATAAATCTAAATTTAAA
1 TTTAAATTTAAAT-TAAATTTAAA
37703 ATAAATTAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 11
0.83 0.03 0.15
Matches are distributed among these distances:
21 2 0.03
22 6 0.10
23 40 0.65
24 14 0.23
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (23 bp):
TTTAAATTTAAATTAAATTTAAA
Found at i:41496 original size:24 final size:23
Alignment explanation
Indices: 41468--41524 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
41458 ACATTATTTG
*
41468 TGAACTTGTTTAATTAAATGTTCA
1 TGAACATGTTT-ATTAAATGTTCA
* * *
41492 TGAACATGTTTGTTTAATGTTCG
1 TGAACATGTTTATTAAATGTTCA
41515 TGAACATGTT
1 TGAACATGTT
41525 CGATTAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 19 0.66
24 10 0.34
ACGTcount: A:0.28, C:0.09, G:0.18, T:0.46
Consensus pattern (23 bp):
TGAACATGTTTATTAAATGTTCA
Found at i:41531 original size:23 final size:23
Alignment explanation
Indices: 41484--41531 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
41474 TGTTTAATTA
* *
41484 AATGTTCATGAACATGTTTGTTT
1 AATGTTCATGAACATGTTCGATT
*
41507 AATGTTCGTGAACATGTTCGATT
1 AATGTTCATGAACATGTTCGATT
41530 AA
1 AA
41532 GTTAAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (23 bp):
AATGTTCATGAACATGTTCGATT
Found at i:48199 original size:9 final size:8
Alignment explanation
Indices: 48184--48225 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 8
48174 AAGTTGTGTA
48184 AGTCAGTT
1 AGTCAGTT
48192 AGTACAGTT
1 AGT-CAGTT
48201 AGT-AGTT
1 AGTCAGTT
*
48208 AGACAGTT
1 AGTCAGTT
48216 ATGTCAGTT
1 A-GTCAGTT
48225 A
1 A
48226 ACATTTGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
7 6 0.21
8 8 0.28
9 15 0.52
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.36
Consensus pattern (8 bp):
AGTCAGTT
Found at i:52697 original size:9 final size:8
Alignment explanation
Indices: 52682--52723 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 8
52672 AAGTTGTGTA
52682 AGTCAGTT
1 AGTCAGTT
52690 AGTACAGTT
1 AGT-CAGTT
52699 AGT-AGTT
1 AGTCAGTT
*
52706 AGACAGTT
1 AGTCAGTT
52714 ATGTCAGTT
1 A-GTCAGTT
52723 A
1 A
52724 ACATTTGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
7 6 0.21
8 8 0.28
9 15 0.52
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.36
Consensus pattern (8 bp):
AGTCAGTT
Done.